Category

This document summarises the current list of existing Web services that we intend to harness in the bioinformatics theme of the OpenKnowledge project. For most of these we provide a link to the WSDL interface that we can use as the connection point between LCC interaction models and the service itself (via constraints in the LCC models). As OpenKnowledge proceeds this list will be adapted. For more information on the list and its maintenance contact Xueping Quan (xquan@inf.ed.ac.uk).

Category	Web Service	Description
Literature and Ontologies	Whatizit(EBI)	A text processing system that allows you to do textmining tasks on text. (wsdl file not available)
	Ontology Lookup(EBI)	OLS provides a web service interface to query multiple ontologies from a single location with a unified output format.
	CitExplorer(EBI)	A number of web services are available to retrieve data from the Citation database.
	GO (DDBJ)	Gene Ontology (GO) provides a controlled vocabulary to describe gene and gene product attributes in any organism.

Sequence Signature Analysis	InterproScan(EBI)	InterProScan, protein domain identifier, a tool that combines different protein signature recognition methods native to the InterPro member databases into one resource with look up of corresponding InterPro and GO annotation
	SeqVISTA(zhiping)	A new module of integrated computational tools for studying transcriptional regulation.(n/a)
	Promoser (zhiping)	Human, Mouse and Rat promoter extraction service
	RepeatMasker(zhiping)	Screens DNA sequences for interspersed repeats and low complexity DNA sequences (n/a)
	POSSUM(zhiping)	Detect cis-elements in DNA sequences
	Clover(zhiping)	A program for identifying functional sites in DNA sequences
	MotifScanner(zhiping)	A program that can be used to screen DNA sequences with precompiled motif models
	GLAM(zhiping)	A program for discovering functional motifs shared by a set of nucleotide sequences
	MotifSampler(zhiping)	A Gibbs sampling based motif finding algorithm
	Cluster-Buster(zhiping)	Finding dense clusters of motifs in DNA sequences.
	PML (DDBJ)	It assemble and analyze SNPs data from distributed heterogeneous database in XML documents described by PML
	SPS (DDBJ)	A splicing profile similarity (SPS) index, which measures relative exon length discrepancy

Pair-wise Alignment	Emboss(EBI)	Use the Water and Needle methods for pair-wise alignment

Multiple Alignment	Muscle(EBI)	The Multiple Sequence Comparison by Log-Expectation.
	ClustalW(EBI)	A progressive global multiple alignment tool for DNA and protein sequences.
	TCoffee(EBI)	A progressive multiple sequence alignment program.
	KAlign(EBI)	A fast and accurate multiple sequence alignment algorithm.
	Mafft(EBI)	A high speed multiple sequence alignment program.

Homology Searching	Fasta(EBI)	Used for a fast protein comparison or a fast nucleotide comparison.
	WU-Blast(EBI)	Used to compare a novel sequence with those contained in nucleotide and protein databases.
	NCBI Blast(EBI)	Used to compare a novel sequence with those contained in nucleotide and protein databases.
	PSI-Blast(EBI)	Position specific iterative / Pattern Hit Initiated Blast
	MPsrch(EBI)	A biological sequence sequence comparison tool that implements Smith and Waterman algorithm
	ScanPS(EBI)	A program for comparing a protein sequence to a database of protein sequences.
	BLAST (DDBJ) (blastdemo)	Used to compare a novel sequence with those contained in nucleotide and protein databases.
	FASTA (DDBJ)	Used for a fast protein comparison or a fast nucleotide comparison.

Data Retrieval	XEMBL (EBI)	A service to display data from the EMBL Nucleotide Sequence Database in XML formats, BSML and AGAVE
	Dbfetch (EBI)	Allows you to retrieve entries from various up-to-date biological databases.
	MSD API(EBI)	Access to data and tools from the Macromolecular Structures Database.
	ChEBI(EBI)	Allows you to retrieve entries from the ChEBI database.
	Integr8(EBI)	Access to a subset of the data available from the Integr8 Web Portal.
	Entrez Utilities(NCBI) (Lite version of E-Utilities (no EFetch); EFetch Web Service; EFetch Web Service for PubMed and nlmCatalog only.)	A federated search engine that allows users to search many discrete health sciences databases, maintained by the National Center for Biotechnology Information with a single query string and user interface. It includes EGQuery, EFetch, EInfo, ELink, ESearch, ESpell, and ESummary utilities
	SRS (DDBJ)	Sequence retrieval system
	ARSA (DDBJ)	all-round retrieval of sequence and annotation in database DDBJ
	GetEntry (DDBJ)	Data retrieval by accession number etc.
	Txsearch (DDBJ)	Execute Taxonomy Database search specified with taxonomy name
	VecScreen (DDBJ)	DDBJ Vector Screening System

Genome Analysis	GIB (DDBJ)	Genome information broker: search selected genomes at once
	GTOP (DDBJ)	A database consists of data analyses of proteins identified by various genome projects It uses sequence homology analyses and features extensive utilization of information on three-dimensional structures
	ENSEMBLE (DDBJ)	Ensembl Genome Browser produces and maintains automatic annotation on selected eukaryotic genomes
	MAPPING (DDBJ)	Map a sequence to mouse genome

Structural Comparison	Dalilite(EBI)	A program for pair-wise structure comparison.
	SSM(EBI)	A service for comparing protein structures in 3D. (no wsdl file)
	GASH (PDBJ)	A robust method for aligning protein structures by maximizing the Number of Equivalent Residues

Structure Modelling	Maxsprout (EBI)	A fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace.

Microarray	BioMart( EBI)	n/a
	GeneCruiser (MIT)	GeneCruiser: a web service for the annotation of microarray data
	SemBiosphere(Yale)	A Semantic Web Approach to Recommending Microarray Clustering Services(n/a)

DataBase	DDBJ	DNA Data Bank in Japan
	PDBJ	Protein Structure DataBank
	BIND	Biomolecular Interaction Network Database
	Pfam	A collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families
	OMIM (DDBJ)	This database is a catalog of human genes and genetic disorders.
	RefSeq (DDBJ)	The NCBI Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms.
	NCBI Genome Annotation (DDBJ)	Assembled and annotated genomes available via GenBank, EMBL and DDBJ.

"omic" data interpreter	GoMiner	GoMiner: a resource for biological interpretation of genomic and proteomic data
"omic" data interpreter	KEGG	Kyoto Encyclopedia of Genes and Genomes

system biology language	BASIS	Biology of Ageing e-Science Integration and Simulation System

Integration	BioMOBY	Integrate distributed heterogeneous bioinformatics web services
	myGrid	Data and application integration such as resource discovery, workflow enactment and distributed query processing
	PathPort(VBI)	Gateway to Distributed Data Management and Computing: The PathPort/ToolBus Framework

List of Baseline Services